Ancient DNA continues to pour in, most recently from a large megalithic burial site in Spain. The mtDNA mix in the gene pool there differs from the modern European gene pool mostly in its low frequency of mtDNA haplogroup H which is the most common mtDNA type in H.
Ancient DNA has made it increasingly clear that most of the modern European haplotypes of Y-DNA R1a and R1b in Europe mostly arrived sometime between 5,000 and 4,000 years ago. But, the evidence that frequency of mtDNA haplogroup H increased in connection with the same demographic transition has been less definitive, although this appears to be the best explanation.
The new megalithic mtDNA from Spain isn't absolutely decisive on that point. The sample size is small enough that an atypical mtDNA mix could be due to random chance (although as you look to the complete corpus of megalithic mtDNA in Europe this becomes an increasingly difficult case to make), and the vicinity where this sample was found has below average frequencies of mtDNA H even today.
But, the mtDNA H haplotype present in two samples pre-3000 BCE (H3) was different than one from 2500 BCE (H1) in the same area, again, suggesting some sort of demographic transition in that time frame which coincides with the expansion of selection Y-DNA R1b haplogroups in Western Europe.
The consistency of the trend towards more mtDNA H almost everywhere in Europe does point to an increase in frequency at around the same time (framed in ever great resolution by finds such as this one) as the demographic events that made select haplogroups of Y-DNA R1a and R1b dominant in much of Europe, is certainly suggestive of the possibility that the trend is real and has a common cause.
It is not the same story, because mtDNA H was present at measurable frequencies in Mesolithic Southern Europe and in early Neolithic Europe, albeit as levels lower than today, while Y-DNA R1a and R1b were found in Europe in those time frames only in trace frequencies relative to the overall available ancient Y-DNA pool. So, for example, the data are consistent with a narrative in which an expansion of these Y-DNA haplogroups involved descendants of migrating men from the steppe married to indigenous women from the Mesolithic era or earlier with mtDNA H whose mtDNA type increased in frequency due to founder effects.
The Spanish site is also notable for having a particularly substantial proportion of mtDNA U5, U4 and V, all of which are conventionally associated with Mesolithic European hunter-gatherers, rather than Neolithic European migrants. There seems to be, more generally, in Iberia, a tendency for there to be more Paleolithic continuity than in many other parts of Europe, perhaps because of its proximity to the Franco-Cantrabrian refugia from which much of Western Europe was repopulated following the Last Glacial Maximum.
The complete disappearance of mtDNA H3, U5, U4 and V from the 2500 BCE sample in the same area is quite notable, as those mtDNA haplogroups made up 48% of the earlier samples, suggesting something more than random sampling chance.